Expression-based clustering of CAZyme-encoding genes of Aspergillus niger

The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. We aim to evaluate co-regulation/co-expression of characterized and putative CAZymes to gain more insight in the function of uncharacterized CAZyme encoding genes in plant biomass utilization and to identify new targets of transcriptional regulators. The focus of the study was on the initial response of A. niger to the presence of a carbon source. For this, microarray data were analyzed of A. niger N402 (wild type) that was grown on a set of 23 carbon sources (including eight monosaccharides, two oligosaccharides, 11 polysaccharides, a crude plant biomass substrate and ferulic acid), and of regulatory mutant strains (ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX) that were grown on their specific inducing compounds. Biological duplicates were grown for each of the conditions and Affymetrix microarray experiments were performed on these samples.